PDB format dictates that TER records are present at the end of a polymer chain.
Chain breaks or non-sequential numbering do not introduce TER records. A TER
record is required between the polymer and non-polymer chain - even with same
chain ID. TER records should not be between non-polymers...
It would be nice to have a setting that adds TER records only where the
chain or segi change (as opposed to whenever the residue numbers are
non-sequential). I believe that better captures the original intent for
terminating polymers. Of course, the real answer is that everyone should
switch to mmC
Hi Marko and Rui,
The TER records can also be prevented with "set pdb_use_ter_records, off".
https://pymolwiki.org/index.php/pdb_use_ter_records
Cheers,
Thomas
On 28 Nov 2016, at 05:03, Rui Sousa wrote:
> Hi Marko,
>
> For the order of the atoms, check if "retain_order" is set to 1; if not
Hi Thomas,
Yeah, this one catches me off-guard now and again. Chain labels were made
case-sensitive, as assemblies sometimes become so large that more than 26
labels are required. So, you'll probably need to specify 'chain A' in stead
of 'chain a'.
Hope it helps,
Tsjerk
On Mon, Nov 28, 2016 at
Hi Marko,
For the order of the atoms, check if "retain_order" is set to 1; if not,
use "set retain_order, 1" before importing your PDB file. For the rest
of your problem, what exactly is being changed from the imported PDB
file and the saved one? Apart from the addition of TER, which is a
fair
Hello everybody,
I'm working with a protein-protein complex and am fixing some stuff.
When I save the fixed complex as a pdb the PDB format is not the same as it was
in the imported pdb files (there it was the same as the CHARMM default pdb
format).
In the saved pdb it changed the line positio
